Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Parsing VariantEval data

TristanTristan La Jolla, CAMember ✭✭
edited January 2015 in Ask the GATK team

VariantEval follows a strict format that is human readable but also the top few lines of each table more than hint that it's ready to be parsed by something else. Been wondering what that is, looks like Python... Is there a nice quick way to load all of these data into something like R or Python? I can imagine using grep to put each table into a file and load that into R but if the output was designed for a certain tool, it would be great to use that.

Thanks as always for the wonderful tools!

Example, what language or tool is this stuff for?

#:GATKTable:11:12:%s:%s:%s:%s:%s:%d:%d:%d:%.2f:%d:%.2f:;

#:GATKTable:CompOverlap:The overlap between eval and comp sites

Tagged:

Answers

Sign In or Register to comment.